GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Angles, Renzo; Arenas-Salinas, Mauricio; García, Roberto; Reyes-Suarez, Jose Antonio; Pohl, Ehmke

Abstract

Background: In the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interaction and protein function. This paper presents GSP4PDB, a bioinformatics web tool that enables the user to visualize, search and explore protein-ligand structural patterns within the entire Protein Data Bank. Results: We introduce the notion of graph-based structural pattern (GSP) as an abstract model for representing protein-ligand interactions. A GSP is a graph where the nodes represent entities of the protein-ligand complex (amino acids and ligands) and the edges represent structural relationships (e.g. distances ligand - amino acid). The novel feature of GSP4PDB is a simple and intuitive graphical interface where the user can “draw” a GSP and execute its search in a relational database containing the structural data of each PDB entry. The results of the search are displayed using the same graph-based representation of the pattern. The user can further explore and analyse the results using a wide range of filters, or download their related information for external post-processing and analysis. Conclusions: GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

Citation

Angles, R., Arenas-Salinas, M., García, R., Reyes-Suarez, J. A., & Pohl, E. (2020). GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. BMC Bioinformatics, 21(S2), Article 85. https://doi.org/10.1186/s12859-020-3352-x

• Journal Article Type: Article
• Online Publication Date: Mar 11, 2020
• Publication Date: 2020
• Deposit Date: Apr 1, 2020
• Publicly Available Date: Apr 2, 2020
• Journal: BMC Bioinformatics
• Electronic ISSN: 1471-2105
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 21
• Issue: S2
• Article Number: 85
• DOI: https://doi.org/10.1186/s12859-020-3352-x
• Public URL: https://durham-repository.worktribe.com/output/1274205